rs1470325

Variant names:

• chr18-50746921-C-T
• rs1470325

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.469 in 151,946 control chromosomes in the GnomAD database, including 18,352 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.47 (18352 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71293 AN: 151828 Hom.: 18362 Cov.: 31

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.506

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.469 AC: 71291 AN: 151946 Hom.: 18352 Cov.: 31 AF XY: 0.473 AC XY: 35147 AN XY: 74274

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.505

Alfa AF: 0.508 Hom.: 3274

Bravo AF: 0.453

Asia WGS AF: 0.509 AC: 1768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.97
DANN	Benign	0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1470325; hg19: chr18-48273291;